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71 lines
2.2 KiB
Python
71 lines
2.2 KiB
Python
#!/usr/bin/env python
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"""
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Connects to a UCSC table browser and scrapes chrominfo for every build
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specified by an input file (such as one output by parse_builds.py).
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If not input file specified, it will connect using parse_builds.py to
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retrieve a list of available builds.
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All chromInfo is placed in a path with the convention
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{dbpath}/buildname.len
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Usage:
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python build_chrom_db.py dbpath/ [builds_file]
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"""
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import sys
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import parse_builds
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import urllib
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import fileinput
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def getchrominfo(url, db):
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tableURL = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
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URL = tableURL + urllib.urlencode({
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"clade" : "",
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"org" : "",
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"db" : db,
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"hgta_outputType": "primaryTable",
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"hgta_group" : "allTables",
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"hgta_table" : "chromInfo",
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"hgta_track" : db,
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"hgta_regionType":"",
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"position":"",
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"hgta_doTopSubmit" : "get info"})
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page = urllib.urlopen(URL)
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for line in page:
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line = line.rstrip( "\r\n" )
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if line.startswith("#"): continue
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fields = line.split("\t")
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if len(fields) > 1:
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yield [fields[0], fields[1]]
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if __name__ == "__main__":
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if len(sys.argv) == 1:
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print "Path to place chromInfo tables must be specified."
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sys.exit(1)
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dbpath = sys.argv[1]
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builds = []
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if len(sys.argv) > 2:
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try:
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buildfile = fileinput.FileInput(sys.argv[2])
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for line in buildfile:
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if line.startswith("#"): continue
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builds.append(line.split("\t")[0])
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except:
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print "Bad input file."
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sys.exit(1)
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else:
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try:
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for build in parse_builds.getbuilds("http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn"):
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builds.append(build[0])
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except:
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print "Unable to retrieve builds."
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sys.exit(1)
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for build in builds:
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if build == "?":continue # no lengths for unspecified chrom
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outfile = open(dbpath + build + ".len", "w")
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print "Retrieving "+build
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for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?",build):
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print >> outfile,"\t".join(chrominfo)
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outfile.close()
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